# psm-convert

## Usage:

`crux psm-convert [options] <input PSM file> <output format>`

## Description:

Reads in a file containing peptide-spectrum matches (PSMs) in one of the variety of supported formats and outputs the same PSMs in a different format

## Input:

- `input PSM file` – The name of a PSM file in tab-delimited text, SQT, pepXML or mzIdentML format
- `output format` – The desired format of the output file. Legal values are tsv, html, sqt, pin, pepxml, mzidentml.

## Output:

The program writes files to the folder `crux-output` by default. The name of the output folder can be set by the user using the `--output-dir` option. The following files will be created:

- `psm-convert.log.txt` – a log file containing a copy of all messages that were printed to stderr.
- `psm-convert.params.txt` – a file containing the name and value of all parameters/options for the current operation. Not all parameters in the file may have been used in the operation. The resulting file can be used with the --parameter-file option for other crux programs.

## Options:

- ### psm-convert options

  - `--input-format auto|tsv|sqt|pepxml|mzidentml` – Legal values are auto, tsv, sqt, pepxml or mzidentml format. Default = `auto`.
  - `--distinct-matches T|F` – Whether matches/ion are distinct (as opposed to total). Default = `true`.
  - `--protein-database <string>` – The name of the file in FASTA format. Default = `<empty>`.

- ### Input and output

  - `--output-dir <string>` – The name of the directory where output files will be created. Default = `crux-output`.
  - `--overwrite T|F` – Replace existing files if true or fail when trying to overwrite a file if false. Default = `false`.
  - `--parameter-file <string>` – A file containing parameters. See the parameter documentation page for details. Default = `<empty>`.
  - `--verbosity <integer>` – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = `30`.